Setting up the parameter file

You can find a ready-to-use parameter file named

params.py

in the tutorial directory.

The file is in the Python format and contains the following content:

protocol = 'denovo_MC-SA'

SA_schedule = [
    (50000,   10000),
    (10000,   10000),
    (5000,   10000),
    (1000,   50000),
    (100,   50000)
]

do_ini_opt = True
ini_opt_SA_schedule = [
    (1000, 1000)
]

traj_frame_period = 10
print_frame_period = traj_frame_period

print_log_scores_to_files = True
print_log_scores_to_files_frame_period = 10

print_total_score_to_files = True
print_total_score_to_files_frame_period = 10


struct_resolutions = [0,10]
add_rbs_from_pdbs = True
connectivity_restraint_weight = 1.
conn_first_copy_only = True

add_symmetry_constraints = True


add_xlink_restraints = True
x_xlink_score_type = 'LogHarmonic'
x_min_ld_score = 25
x_weight = 1000.0
x_xlink_distance = 15

discrete_restraints_weight=10000

ev_restraints = [
    {
        'name': 'ev_restraints_lowres',
        'weight': 10,
        'repr_resolution': 10
    }
]

scoring_functions = {
    'score_func_ini_opt': {
        'restraints': [
            'discrete_restraints',
            'conn_restraints',
            'ev_restraints_lowres'
        ]
    },
    'score_func_lowres': {
        'restraints': [
            'discrete_restraints',
            'xlink_restraints',
            'conn_restraints',
            'ev_restraints_lowres'
        ]
    }
}

score_func = 'score_func_lowres'
score_func_ini_opt = 'score_func_ini_opt'

ntasks = 1
cluster_submission_command = 'sbatch'
from string import Template
run_script_templ = Template("""#!/bin/bash
#
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=$ntasks
#SBATCH --mem-per-cpu=2000
#SBATCH --job-name=${prefix}fit
#SBATCH --time=00:30:00
#SBATCH -e $outdir/logs/${prefix}_err.txt
#SBATCH -o $outdir/logs/${prefix}_out.txt

echo "Running on:"
srun hostname

$cmd

wait
""")

To generate this file yourself from scratch:

1. Download the template params_combinations.py file

2. Open the file in an editor to adjust the parameters as in the provided example.

   See parameters for explanations and description of available parameters.